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diskin-lab-chop
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AutoGVP
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Bug: incorrect column classes assigned when loading autogvp output
#150
rjcorb
closed
1 year ago
0
Set resolved ClinVar calls to Stars == "1"
#149
rjcorb
closed
1 year ago
0
Bug: ClinVar calls with conflicting interpretations have NA clinvar stars
#148
rjcorb
closed
1 year ago
0
rm duplicate cols in intervar/multianno dfs
#147
rjcorb
closed
1 year ago
0
Bug: duplicated columns in autogvp output
#146
rjcorb
closed
1 year ago
0
Select AutoPVS1 transcript as final variant annotation
#145
rjcorb
closed
1 year ago
1
Feature request: use AutoPVS1 transcript annotation in final output
#144
rjcorb
closed
1 year ago
0
Filter multianno, autopvs1, intervar files before loading in R
#143
rjcorb
closed
1 year ago
1
Feature request: filter annotation files prior to loading in R
#142
rjcorb
closed
1 year ago
0
create var id cols to match multianno & intervar variants
#141
rjcorb
closed
1 year ago
0
Bug: intervar and annovar files not matched by variant id
#140
rjcorb
closed
1 year ago
0
modify clinvar star assignment for no interpretation variants
#139
rjcorb
closed
1 year ago
0
Bug: ClinVar entries with no assertion for individual variant have Stars==NA
#138
rjcorb
closed
1 year ago
0
Feature request: modify loading and modification of input files in 04-filter-gene-annotations.R
#137
rjcorb
closed
1 year ago
0
modify loading of annotation files
#136
rjcorb
closed
1 year ago
0
update address_conflicting_interp()
#135
rjcorb
closed
1 year ago
0
update clinvar star assignment code
#134
rjcorb
closed
1 year ago
5
Bug: variants not in ClinVar database have clinvar_stars == 0
#133
rjcorb
closed
1 year ago
0
Feature request: optimize modifying of ClinVar vcf file
#132
rjcorb
closed
1 year ago
0
Feature request: optimize reading and modifying multianno, intervar, and autopvs1 dfs
#131
rjcorb
closed
1 year ago
0
Feature request: modify address_conflicting_intrep() function to only loop through 1NR variants
#130
rjcorb
closed
1 year ago
0
cleaned comments
#129
naqvia
closed
1 year ago
1
Fix filter vcf script so first filtering criterion is applied
#128
rjcorb
closed
1 year ago
0
Bug: First filtering criterion skipped
#127
rjcorb
closed
1 year ago
0
Set clinvar clinsig equal to clinvar final call
#126
rjcorb
closed
1 year ago
1
Bug: Clinvar final call does not match clinvar_clinsig
#125
rjcorb
closed
1 year ago
0
Modify address_ambiguous_calls() function to exclude likely pathogenic clinvar calls
#124
rjcorb
closed
1 year ago
0
readme update
#123
naqvia
closed
1 year ago
2
Bug: Variants with resolved ClinVar calls are reporting Intervar call in final output
#122
rjcorb
closed
1 year ago
1
Add new test file that captures different scenarios
#121
jungkim2
closed
1 year ago
9
adding new test file with potential scenarios for variant classification
#120
jungkim2
closed
1 year ago
1
Feature request: extract VEP CSQ field names from VCF
#119
rjcorb
closed
1 year ago
1
Update 01-annotate_variants_custom_input.R
#118
jungkim2
closed
1 year ago
10
Issue116
#117
naqvia
closed
1 year ago
0
Bug: ClinVar 1NR not getting consensus calls
#116
jungkim2
closed
1 year ago
3
Bug:InterVar when there is both pathogenic and benign code
#115
jungkim2
closed
1 year ago
1
Feature request: code cleanup
#114
jharenza
closed
1 year ago
1
modified code to address issue111
#113
naqvia
closed
1 year ago
1
deleted file
#112
naqvia
closed
1 year ago
0
Bug:0 stars getting wrong classification
#111
jungkim2
closed
1 year ago
5
Update 01-annotate_variants_custom_input.R
#110
jungkim2
closed
1 year ago
1
Update 01-annotate_variants_custom_input.R
#109
jungkim2
closed
1 year ago
0
Update 01-annotate_variants_custom_input.R
#108
jungkim2
closed
1 year ago
0
Bug: InterVar classified variants downgrade to LP when autoPVS1 gives very strong
#107
jungkim2
closed
1 year ago
3
Remove output file in AutoGVP dir
#106
jharenza
closed
1 year ago
1
Add script to select clinVar variant submissions
#105
rjcorb
closed
1 year ago
4
Feature request: consolidate ClinVar submission calls prior to running AutoGVP
#104
rjcorb
closed
1 year ago
1
Feature request:adding criterion field (in autoPVS1 file) in the final output
#103
jungkim2
closed
1 year ago
1
Bug: ClinVar 1NR not getting most recent
#102
jungkim2
closed
1 year ago
2
Bug: autoPVS1 unmet but still getting P/LP
#101
jungkim2
closed
1 year ago
3
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